You can purchase these pokemon with pokedollars (via auction) or other pokemon
Shinies:
Shiny azurill
Shiny basculin (red stripe)
Shiny Cutiefly
Shiny darumaka
Shiny duraladon
Shiny dwebble
Shiny houndoor
Shiny magikarp
Shiny murkrow
Shiny onix (2x)
Shiny steelix
Shiny pancham
Shiny relicanth (2x)
Shiny rookidee
Shiny sizzilpeede
Shiny solrock
Shiny stantler
Shiny stonjourner
Shiny torkoal
Shiny whismur
Shiny zubat (2x)
Legendaries (100k+ or other pokemon)
Mystic groudon
Dark mewtwo